<html xmlns:v="urn:schemas-microsoft-com:vml" xmlns:o="urn:schemas-microsoft-com:office:office" xmlns:w="urn:schemas-microsoft-com:office:word" xmlns:m="http://schemas.microsoft.com/office/2004/12/omml" xmlns="http://www.w3.org/TR/REC-html40">
<head>
<meta http-equiv="Content-Type" content="text/html; charset=utf-8">
<meta name="Generator" content="Microsoft Word 15 (filtered medium)">
<!--[if !mso]><style>v\:* {behavior:url(#default#VML);}
o\:* {behavior:url(#default#VML);}
w\:* {behavior:url(#default#VML);}
.shape {behavior:url(#default#VML);}
</style><![endif]--><style><!--
/* Font Definitions */
@font-face
{font-family:Helvetica;
panose-1:0 0 0 0 0 0 0 0 0 0;}
@font-face
{font-family:"Cambria Math";
panose-1:2 4 5 3 5 4 6 3 2 4;}
@font-face
{font-family:Calibri;
panose-1:2 15 5 2 2 2 4 3 2 4;}
@font-face
{font-family:Verdana;
panose-1:2 11 6 4 3 5 4 4 2 4;}
/* Style Definitions */
p.MsoNormal, li.MsoNormal, div.MsoNormal
{margin:0in;
margin-bottom:.0001pt;
font-size:11.0pt;
font-family:"Calibri",sans-serif;}
a:link, span.MsoHyperlink
{mso-style-priority:99;
color:#0563C1;
text-decoration:underline;}
a:visited, span.MsoHyperlinkFollowed
{mso-style-priority:99;
color:#954F72;
text-decoration:underline;}
p.msonormal0, li.msonormal0, div.msonormal0
{mso-style-name:msonormal;
mso-margin-top-alt:auto;
margin-right:0in;
mso-margin-bottom-alt:auto;
margin-left:0in;
font-size:11.0pt;
font-family:"Calibri",sans-serif;}
span.apple-tab-span
{mso-style-name:apple-tab-span;}
span.EmailStyle19
{mso-style-type:personal-reply;
font-family:"Calibri",sans-serif;
color:windowtext;}
.MsoChpDefault
{mso-style-type:export-only;
font-size:10.0pt;}
@page WordSection1
{size:8.5in 11.0in;
margin:1.0in 1.0in 1.0in 1.0in;}
div.WordSection1
{page:WordSection1;}
--></style><!--[if gte mso 9]><xml>
<o:shapedefaults v:ext="edit" spidmax="1026" />
</xml><![endif]--><!--[if gte mso 9]><xml>
<o:shapelayout v:ext="edit">
<o:idmap v:ext="edit" data="1" />
</o:shapelayout></xml><![endif]-->
</head>
<body lang="EN-US" link="#0563C1" vlink="#954F72">
<div class="WordSection1">
<p class="MsoNormal">Hi Eric,<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">That looks pretty much what I needed. Thanks for the prompt response also for the point making about the atom type changes.<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">Best regards,<o:p></o:p></p>
<p class="MsoNormal">Kiruba<o:p></o:p></p>
<p class="MsoNormal"><o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<div style="border:none;border-top:solid #B5C4DF 1.0pt;padding:3.0pt 0in 0in 0in">
<p class="MsoNormal"><b><span style="font-size:12.0pt;color:black">From: </span></b><span style="font-size:12.0pt;color:black">Eric Pettersen <pett@cgl.ucsf.edu><br>
<b>Reply-To: </b>"chimera-users@cgl.ucsf.edu BB" <chimera-users@cgl.ucsf.edu><br>
<b>Date: </b>Friday, December 6, 2019 at 2:28 PM<br>
<b>To: </b>"Palani, Kirubakaran" <Kirubakaran.Palani@fccc.edu><br>
<b>Cc: </b>"chimera-users@cgl.ucsf.edu" <chimera-users@cgl.ucsf.edu><br>
<b>Subject: </b>Re: [Chimera-users] pseudobond problem while writing mol2 format<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><o:p> </o:p></p>
</div>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Verdana",sans-serif;color:red">EXTERNAL MESSAGE. DO NOT open attachments or click links from unknown senders or unknown emails.
</span><o:p></o:p></p>
<div class="MsoNormal" align="center" style="text-align:center">
<hr size="0" width="100%" align="center">
</div>
<p class="MsoNormal"><o:p> </o:p></p>
<div>
<p class="MsoNormal">Hi Kiruba, <o:p></o:p></p>
<div>
<p class="MsoNormal">For each of those pseudobonds, there is a hidden “real” bond. To have the Mol2 file treat the segments as disconnected, the hidden bonds have to be deleted. I have attached a simple Python script that does that. So you would open your
PDB file, run the script (simply opening the .py file will run it) and then save your Mol2.<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal">Keep in mind that deleting those hidden bonds will change the corresponding atom types. So for instance the backbone nitrogens will be given the Mol2 type N.4 (appropriate for N-terminal) rather than N.am (appropriate for amide).<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal"><o:p> </o:p></p>
</div>
<div>
<p class="MsoNormal">—Eric<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal"><o:p> </o:p></p>
<div>
<div>
<p class="MsoNormal"><span style="font-size:9.0pt;font-family:Helvetica;color:black"><br>
<br>
<span class="apple-tab-span"><o:p></o:p></span></span></p>
<p class="MsoNormal"><span style="font-size:9.0pt;font-family:Helvetica;color:black">Eric Pettersen<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:9.0pt;font-family:Helvetica;color:black">UCSF Computer Graphics Lab<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:9.0pt;font-family:Helvetica;color:black"><o:p> </o:p></span></p>
</div>
</div>
</div>
</div>
</div>
<br>
<hr>
<font face="Verdana" color="Red" size="2"><br>
This electronic message is intended to be for the use of the named recipient, and may contain information that is confidential or privileged. This communication may contain protected health information (PHI) that is legally protected from inappropriate disclosure
by the Privacy Standards of the Health Insurance Portability and Accountability Act (HIPAA) and relevant Pennsylvania Laws. You can direct questions concerning PHI or HIPAA to the Corporate Compliance and Privacy Officer at (215) 707-5605. If you are not the
intended recipient, please note that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this message in error, you should notify the sender immediately by telephone or by return e-mail and delete and
destroy all copies of this message.<br>
</font>
</body>
</html>